3.Load your expression data into GSEA. You can
follow the GSEA documentation
on various ways to do so. For a simple experiment, like the 24hr cold-treated
plants vs. control in GSE5534, I
have found it is best to convert the data to a RNK
(Ranked list) file.Based on
statistical analysis such as a T-test, I eliminate genes that are not
significantly different between experiment and control. I often use less
selective cutoffs for P values or Q value in filtering, so that I have a few
hundred to a few thousand genes. The genes are then ranked by fold change and the file saved
in a text file with .rnk as extension in file name.
This is the file
that I used in the paper. Note that runing GSEA using
RNK files needs to be initiated from GSEA main menu Tools GseaPreranked.

4.Another essential file is a .chip file that maps
probe IDs to gene symbols. This information needs to be downloaded from
microarray manufacture. This file is for Affymetrix ATH1 chip.

2.8/27/2012: Corrected duplicate entry in literature
gene sets LIT_SAKUMA_FLUORESCENCE-1H-DROUGHT-STRESS/CONTROL_DN. This causes
GSEA to have errors. The two gene sets are renamed. Literature gene sets and
all gene sets and Excel file updated.

3.8/19/2013: Updated the database AraPath (Database in Arabidopsis). There are a total of
4,774 updated gene sets, including 1,426 literature gene sets from GEO and
ArrayExpress and 3,348 Gene Ontology gene sets.

4.9/8/2013: Added the new database GSKB (Gene Set
Knowledgebase in Mouse), which includes a total of 42,056 gene sets of Mouse.

5.9/11/2013: Added the new database in Yeast, which
includes a total of 8,457 gene sets of Yeast.